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Test replicates

Test replicates #64

Workflow file for this run

name: Run GPU nf-tests
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
workflow_dispatch:
inputs:
runners:
description: "Runners to test on"
type: string
default: "gpu"
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
NFT_VER: "0.9.2"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
# renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
NXF_VER: "24.10.2"
jobs:
get-shards:
runs-on: ubuntu-latest
name: "Get Shards"
outputs:
shard: ${{ steps.set-shards.outputs.shard }}
total_shards: ${{ steps.set-shards.outputs.total_shards }}
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
fetch-depth: 0
- name: run nf-test-shard action
id: set-shards
uses: ./.github/actions/nf-test-shard
env:
NFT_VER: ${{ env.NFT_VER }}
with:
tags: "gpu"
max_shards: 2
- name: Set outputs
id: set-outputs
run: |
echo "shard=${{ steps.set-shards.outputs.shard }}" >> $GITHUB_ENV
echo "total_shards=${{ steps.set-shards.outputs.total_shards }}" >> $GITHUB_ENV
nf-test-gpu:
needs: [get-shards]
runs-on: "gpu"
name: "GPU Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}"
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
strategy:
fail-fast: false
matrix:
profile: [docker, singularity]
shard: ${{ fromJson(needs.get-shards.outputs.shard) }}
NXF_VER:
- "24.10.2"
filters: [pipeline]
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
fetch-depth: 0
- name: Run nf-test Action
uses: ./.github/actions/nf-test
with:
profile: ${{ matrix.profile }},gpu
shard: ${{ matrix.shard }}
total_shards: ${{ needs.get-shards.outputs.total_shards }}
filters: ${{ matrix.filters }}
tags: "gpu"
confirm-pass:
runs-on: ubuntu-latest
needs: [nf-test-gpu]
if: always()
steps:
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1
- name: One or more tests cancelled
if: ${{ contains(needs.*.result, 'cancelled') }}
run: exit 1
- name: All tests ok
if: ${{ contains(needs.*.result, 'success') }}
run: exit 0
- name: debug-print
if: always()
run: |
echo "toJSON(needs) = ${{ toJSON(needs) }}"
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"